1. DNA Sequencing

2. Determining DNA Sequence
Originally 2 methods were invented around 1976, but only one is widely used: the chain-termination method invented by Fred Sanger.
The other method is Maxam-Gilbert chemical degradation method, which is still used for specialized purposes, such as analyzing DNA-protein interactions.
More recently, several cheaper and faster alternatives have been invented. It is hard to know which of these methods, or possibly another method, will ultimately become standard. We will discus two of them: 454 pyrosequencing and Illumina/Solexa sequencing

3. Sanger Sequencing
Uses DNA polymerase to synthesize a second DNA strand that is labeled. DNA polymerase always adds new bases to the 3’ end of a primer that is base-paired to the template DNA.
DNA polymerase is modified to eliminate its editing function
Also uses chain terminator nucleotides: dideoxy nucleotides (ddNTPs), which lack the -OH group on the 3' carbon of the deoxyribose. When DNA polymerase inserts one of these ddNTPs into the growing DNA chain, the chain terminates, as nothing can be added to its 3' end.

4. Sequencing Reaction
The template DNA is usually single stranded DNA, which can be produced from plasmid cloning vectors that contain the origin of replication from a single stranded bacteriophage such as M13 or fd. The primer is complementary to the region in the vector adjacent to the multiple cloning site.
Sequencing is done by having 4 separate reactions, one for each DNA base.
All 4 reactions contain the 4 normal dNTPs, but each reaction also contains one of the ddNTPs.
In each reaction, DNA polymerase starts creating the second strand beginning at the primer.
When DNA polymerase reaches a base for which some ddNTP is present, the chain will either:
terminate if a ddNTP is added, or:
continue if the corresponding dNTP is added.
which one happens is random, based on ratio of dNTP to ddNTP in the tube.
However, all the second strands in, say, the A tube will end at some A base: you get a collection of DNAs that end at each of the A's in the region being sequenced.

5. Electrophoresis
The newly synthesized DNA from the 4 reactions is then run (in separate lanes) on an electrophoresis gel.
The DNA bands fall into a ladder-like sequence, spaced one base apart. The actual sequence can be read from the bottom of the gel up.
Automated sequencers use 4 different fluorescent dyes as tags attached to the dideoxy nucleotides and run all 4 reactions in the same lane of the gel.
Today’s sequencers use capillary electrophoresis instead of slab gels.
Radioactive nucleotides (32P) are used for non-automated sequencing.
Sequencing reactions usually produce about bp of good sequence.

7. Next Generation Sequencing
Recently a number of faster and cheaper sequencing methods have been developed.
The Archon X prize (2006): "the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 (US) per genome.”
Currently there is a push for (and NIH grant money for) developing a method that will sequence the entire human genome for $1000, to allow personal genomics.
One of the most widely used new methods involve the pyrosequencing biochemical reactions (invented by Nyren and Ronaghi in 1996), with the massively parallel microfluidics technology invented by the 454 Life Sciences company. We can call this combined technology “454 sequencing”.
Applications:
sequencing of whole bacterial genomes in a single run
sequencing genomes of individuals
metagenomics: sequencing DNA extracted from environmental samples
looking for rare variants in a single amplified region, in tumors or viral infections
transcriptome sequencing: total cellular mRNA converted to cDNA.

8. Pyrosequencing Biochemistry
In DNA synthesis, a dNTP is attached to the 3’ end of the growing DNA strand. The two phosphates on the end are released as pyrophosphate (PPi).
ATP sulfurylase uses PPi and adenosine 5’-phosphosulfate to make ATP.
ATP sulfurylase is normally used in sulfur assimilation: it converts ATP and inorganic sulfate to adenosine 5’-phosphosulfate and PPi. However, the reaction is reversed in pyrosequencing.
Luciferase is the enzyme that causes fireflies to glow. It uses luciferin and ATP as substrates, converting luciferin to oxyluciferin and releasing visible light.
The amount of light released is proportional to the number of nucleotides added to the new DNA strand.
After the reaction has completed, apyrase is added to destroy any leftover dNTPs.

9. More Pyrosequencing
The four dNTPs are added one at a time, with apyrase degradation and washing in between.
The amount of light released is proportional to the number of bases added. Thus, if the sequence has 2 A’s in a row, both get added and twice as much light is released as would have happened with only 1 A.
The pyrosequencing machine cycles between the 4 dNTPs many times, building up the complete sequence. About 300 bp of sequence is possible (as compared to bp with Sanger sequencing).
The light is detected with a charge-coupled device (CCD) camera, similar to those used in astronomy.
YouTube animation (with music!):

10. 454 Technology
To start, the DNA is sheared into bp fragments, and the ends are “polished” by removing any unpaired bases at the ends.
Adapters are added to each end. The DNA is made single stranded at this point.
One adapter contains biotin, which binds to a streptavidin-coated bead. The ratio of beads to DNA molecules is controlled so that most beads get only a single DNA attached to them.
Oil is added to the beads and an emulsion is created. PCR is then performed, with each aqueous droplet forming its own micro-reactor. Each bead ends up coated with about a million identical copies of the original DNA.

11. More 454 Technology
After the emulsion PCR has been performed, the oil is removed, and the beads are put into a “picotiter” plate. Each well is just big enough to hold a single bead.
The pyrosequencing enzymes are attached to much smaller beads, which are then added to each well.
The plate is then repeatedly washed with the each of the four dNTPs, plus other necessary reagents, in a repeating cycle.
The plate is coupled to a fiber optic chip. A CCD camera records the light flashes from each well.

12. Illumina/Solexa Sequencing
Another high throughput Next Generation Sequencing method.
First we will discuss the sequencing reaction itself, and then deal with how it is done on many sequences simultaneously.

13. Illumina Sequencing Chemistry
this method uses the basic Sanger idea of “sequencing by synthesis” of the second strand of a DNA molecule. Starting with a primer, new bases are added one at a time, with fluorescent tags used to determine which base was added.
The fluorescent tags block the 3’-OH of the new nucleotide, and so the next base can only be added when the tag is removed.
So, unlike pyrosequencing, you never have to worry about how many adjacent bases of the same type are present.
The cycle is repeated times.

14. Illumina Massively Parallel System
The idea is to put 2 different adapters on each end of the DNA, then bind it to a slide coated with the complementary sequences for each primer. This allows “bridge PCR”, producing a small spot of amplified DNA on the slide.
The slide contains millions of individual DNA spots. The spots are visualized during the sequencing run, using the fluorescence of the nucleotide being added.

15. Sequence Assembly
DNA is sequenced in very small fragments: at most, 1000 bp. Compare this to the size of the human genome: 3,000,000,000 bp. How to get the complete sequence?
In the early days (1980’s), genome sequencing was done by chromosome walking (aka primer walking): sequence a region, then make primers from the ends to extend the sequence. Repeat until the target gene was reached.
The cystic fibrosis gene was identified by walking about 500 kbp from a closely linked genetic marker, a process that took a long time and was very expensive.
Still useful for fairly short DNA molecules, say 1-10 kbp.

16. Shotgun Sequencing
Shotgun sequencing is what is typically done today: DNA is fragmented randomly and enough fragments are sequenced so each base is read 10 times or more on average. The overlapping fragments (“reads”) are then assembled into a complete sequence.
For large genomes, hierarchical shotgun sequencing is a useful technique: first break up the genome into an ordered set of cloned fragments (scaffolds), usually BAC clones. Each BAC is shotgun sequenced separately.

17. Assembly Problems
In principle, assembling a sequence is just a matter of finding overlaps and combining them.
In practice:
most genomes contain multiple copies of many sequences,
there are random mutations (either naturally occurring cell-to-cell variation or generated by PCR or cloning),
there are sequencing errors and misreadings,
sometimes the cloning vector itself is sequenced
sometimes miscellaneous junk DNA gets sequenced
Getting rid of vector sequences is easy once you recognize the problem: just check for them.
Repeat sequence DNA is very common in eukaryotes, and sequencing highly repeated regions (such as centromeres) remains difficult even now. High quality sequencing helps a lot: small variants can be reliably identified.
Sequencing errors, bad data, random mutations, etc. were originally dealt with by hand alignment and human judgment. However, this became impractical when dealing with the Human Genome Project.
This led to the development of automated methods. The most useful was the phred/phrap programs developed by Phil Green and collaborators at Washington University in St. Louis.

18. Phred Quality Scores
Phred is a program that assigns a quality score to each base in a sequence. These scores can then be used to trim bad data from the ends, and to determine how good an overlap actually is.
there are much improved algorithms now, but the phred quality score is still widely used.
Phred scores are logarithmically related to the probability of an error: a score of 10 means a 10% error probability; 20 means a 1% chance, 30 means a 0.1% chance, etc.
Q = -10 log P, where Q is the phred score and P is the probability that the base was called incorrectly.
A score of 20 is generally considered the minimum acceptable score.

19. Phred Algorithm
Phred uses Fourier analysis (decomposing the data into a series of sine waves) to examine chromatogram trace data.
First, find the expected position of each peak, assuming they are supposed to be evenly spaced, with no compressions or other factors altering peak positions.
Next, find actual center and area of each peak.
Finally, match observed peaks to expected. This involves splitting some peaks and ignoring others.
Assigning a quality score involves comparing various parameters determined for each peak with data that was generated from known sequences run under a wide variety of conditions (i.e., based on ad hoc observations and not theory).
Since all four traces (A, C, G, T) are examined separately, phred generates a best-guess sequence. Phred output is a file where each line contains one base and its quality score.

20. Combining Sequences with Phrap
Phrap first examines all reads for matching “words”: short sections of identical sequence. The matching words need to be in the same order and spacing.
Sequences in both orientations are examined, using the reverse-complement sequence if necessary.
The entire sequences of pairs with matching words are then aligned using the Smith-Waterman algorithm (a standard technique we will look at later).
Phrap then looks for discrepancies in the combined sequences, using phred scores to decide between alternatives. Phrap generates quality scores from the combined phred data.
Sequencing errors are not necessarily random: homopolymeric regions (several of the same base in a row) are notoriously tricky to sequence accurately. Using the opposite strand often helps resolve these regions. Also using a different sequencing technology or chemistry.
Sequences are combined with a greedy algorithm: all pairs of fragments are scored for the length and quality of their overlap region, and then the largest and best-matched pair is merged. This process is repeated until some minimum score is reached.
The result is a set of contigs: reads assembled into a continuous DNA sequence.
The ideal result is the entire chromosome assembled into a single contig.

21. Finishing the Sequence
Shotgun sequencing of random DNA fragments necessarily misses some regions altogether.
Also, for sequencing methods that involve cloning (Sanger), certain regions are impossible to clone: they kill the host bacteria.
Thus it is necessary to close gaps between contigs, and to re-sequence areas with low quality scores. This process is called finishing. It can take up to 1/2 of all the effort involved in a genome sequencing project.
Mostly hand work: identify the bad areas and sequence them by primer walking.
Sometimes using alternative sequencing chemistries (enzymes, dyes, terminators, dNTPs) can resolve a problematic region.
Once a sequence is completed, it is usually analyzed by finding the genes and other features on it: annotation. We will discuss this later.
Submission of the annotated sequence to Genbank allows everyone access to it: the final step in the scientific method.